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ID Publikation
19180 Al Arab, M., Bernt, M., Höner zu Siederdissen, C., Tout, K., Stadler, P.F. (2017):
Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements
Algorithms Mol. Biol. 12 , art. 22
Volltext (DOI)
24785 Anders, J., Petruschke, H., Jehmlich, N., Haange, S.-B., von Bergen, M., Stadler, P.F. (2021):
A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations
BMC Bioinformatics 22 , art. 277
Volltext (DOI)
23122 Balogh, G., Bernhart, S.H., Stadler, P.F., Schor, J. (2020):
A probabilistic version of Sankoff’s maximum parsimony algorithm
J. Bioinform. Comput. Biol. 18 (1), art. 2050004
Volltext (DOI)
23714 Bedulina, D., Drozdova, P., Gurkov, A., von Bergen, M., Stadler, P.F., Luckenbach, T., Timofeyev, M., Kalkhof, S. (2021):
Proteomics reveals sex-specific heat shock response of Baikal amphipod Eulimnogammarus cyaneus
Sci. Total Environ. 763 , art. 143008
Volltext (DOI)
54 Benkö, G., Centler, F., Dittrich, P., Flamm, C., Stadler, B.M.R., Stadler, P.F. (2009):
A topological approach to chemical organizations
Artif. Life 15 (1), 71 - 88
Volltext (DOI)
18210 Bhattacharya, D.P., Canzler, S., Kehr, S., Hertel, J., Grosse, I., Stadler, P.F. (2016):
Phylogenetic distribution of plant snoRNA families
BMC Genomics 17 , art. 969
Volltext (DOI)
19111 Binder, S., Hösler, N., Riedel, D., Zipfel, I., Buschmann, T., Kämpf, C., Reiche, K., Burger, R., Gramatzki, M., Hackermüller, J., Stadler, P.F., Horn, F. (2017):
STAT3-induced long noncoding RNAs in multiple myeloma cells display different properties in cancer
Sci. Rep. 7 , art. 7976
Volltext (DOI)
22777 Borim Corrêa, F., Saraiva, J.P., Stadler, P.F., Nunes da Rocha, U. (2020):
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes
Nucleic Acids Res. 48 (D1), D626 - D632
Volltext (DOI)
17355 Braasch, I., Gehrke, A.R., Smith, J.J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A.M., Campbell, M.S., Barrell, D., Martin, K.J., Mulley, J.F., Ravi, V., Lee, A.P., Nakamura, T., Chalopin, D., Fan, S., Wcisel, D., Cañestro, C., Sydes, J., Beaudry, F.E.G., Sun, Y., Hertel, J., Beam, M.J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J.H., Litman, G.W., Litman, R.T., Mikami, M., Ota, T., Saha, N.R., Williams, L., Stadler, P.F., Wang, H., Taylor, J.S., Fontenot, Q., Ferrara, A., Searle, S.M.J., Aken, B., Yandell, M., Schneider, I., Yoder, J.A., Volff, J.-N., Meyer, A., Amemiya, C.T., Venkatesh, B., Holland, P.W.H., Guiguen, Y., Bobe, J., Shubin, N.H., Di Palma, F., Alföldi, J., Lindblad-Toh, K., Postlethwait, J.H. (2016):
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
Nature Genet. 48 (4), 427 - 437
Volltext (DOI)
21393 Canzler, S., Stadler, P.F., Hertel, J. (2017):
Evolution of fungal U3 snoRNAs: Structural variation and introns
Non-Coding RNA 3 (1), art. 3
Volltext (DOI)
17254 Canzler, S., Stadler, P.F., Hertel, J. (2016):
U6 snRNA intron insertion occurred multiple times during fungi evolution
RNA Biol. 13 (2), 119 - 127
Volltext (DOI)
20004 Canzler, S., Stadler, P.F., Schor, J. (2018):
The fungal snoRNAome
RNA 24 (3), 342 - 360
Volltext (DOI)
21400 de Araujo Oliveira, J.V., Costa, F., Backofen, R., Stadler, P.F., Walter, M.E.M.T., Hertel, J. (2016):
SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification
BMC Bioinformatics 17 (Suppl 18), art. 464
Volltext (DOI)
22589 Donath, A., Jühling, F., Al-Arab, M., Bernhart, S.H., Reinhardt, F., Stadler, P.F., Middendorf, M., Bernt, M. (2019):
Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes
Nucleic Acids Res. 47 (20), 10543 - 10552
Volltext (DOI)
21932 Drozdova, P., Bedulina, D., Madyarova, E., Rivarola-Duarte, L., Schreiber, S., Stadler, P.F., Luckenbach, T., Timofeyev, M. (2019):
Description of strongly heat-inducible heat shock protein 70 transcripts from Baikal endemic amphipods
Sci. Rep. 9 , art. 8907
Volltext (DOI)
22169 Drozdova, P., Rivarola-Duarte, L., Bedulina, D., Axenov-Gribanov, D., Schreiber, S., Gurkov, A., Shatilina, Z., Vereshchagina, K., Lubyaga, Y., Madyarova, E., Otto, C., Jühling, F., Busch, W., Jakob, L., Lucassen, M., Sartoris, F.J., Hackermüller, J., Hoffmann, S., Pörtner, H.-O., Luckenbach, T., Timofeyev, M., Stadler, P.F. (2019):
Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods
BMC Genomics 20 , art. 712
Volltext (DOI)
17663 Fontenot, Q., Ferrara, A., Searle, S.M.J., Aken, B., Yandell, M., Schneider, I., Yoder, J.A., Volff, J.-N., Meyer, A., Amemiya, C.T., Venkatesh, B., Holland, P.W.H., Guiguen, Y., Bobe, J., Shubin, N.H., Di Palma, F., Alföldi, J., Lindblad-Toh, K., Postlethwait, J.H., Martin, K.J., Mulley, J.F., Ravi, V., Lee, A.P., Nakamura, T., Chalopin, D., Fan, S., Wcisel, D., Cañestro, C., Sydes, J., Beaudry, F.E.G., Sun, Y., Hertel, J., Beam, M.J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J.H., Litman, G.W., Litman, R.T., Mikami, M., Ota, T., Saha, N.R., Williams, L., Stadler, P.F., Wang, H., Taylor, J.S., Braasch, I., Gehrke, A.R., Smith, J.J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A.M., Campbell, M.S., Barrell, D. (2016):
Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons (vol 48, pg 427, 2016). Corrected after print 25 April 2016
Nature Genet. 48 (6), 700 - 700
Volltext (DOI)
22003 Gurkov, A., Rivarola-Duarte, L., Bedulina, D., Fernández Casas, I., Michael, H., Drozdova, P., Nazarova, A., Govorukhina, E.B., Timofeyev, M., Stadler, P.F., Luckenbach, T. (2019):
Indication of ongoing amphipod speciation in Lake Baikal by genetic structures within endemic species
BMC Evol. Biol. 19 , art. 138
Volltext (DOI)
14688 Hackermüller, J., Reiche, K., Otto, C., Hösler, N., Blumert, C., Brocke-Heidrich, K., Böhlig, L., Nitsche, A., Kasack, K., Ahnert, P., Krupp, W., Engeland, K., Stadler, P.F., Horn, F. (2014):
Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein coding RNAs
Genome Biol. 15 (3), R48
Volltext (DOI)
14689 Hoffmann, S., Otto, C., Doose, G., Tanzer, A., Langenberger, D., Christ, S., Kunz, M., Holdt, L.M., Teupser, D., Hackermüller, J., Stadler, P.F. (2014):
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
Genome Biol. 15 (2), R34
Volltext (DOI)
18004 Hölzer, M., Krähling, V., Amman, F., Barth, E., Bernhart, S.H., Carmelo, V.A.O., Collatz, M., Doose, G., Eggenhofer, F., Ewald, J., Fallmann, J., Feldhahn, L.M., Fricke, M., Gebauer, J., Gruber, A.J., Hufsky, F., Indrischek, H., Kanton, S., Linde, J., Mostajo, N., Ochsenreiter, R., Riege, K., Rivarola-Duarte, L., Sahyoun, A.H., Saunders, S.J., Seemann, S.E., Tanzer, A., Vogel, B., Wehner, S., Wolfinger, M.T., Backofen, R., Gorodkin, J., Grosse, I., Hofacker, I., Hoffmann, S., Kaleta, C., Stadler, P.F., Becker, S., Marz, M. (2016):
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells
Sci. Rep. 6 , art. 34589
Volltext (DOI)
24313 Jakob, L., Vereshchagina, K.P., Tillmann, A., Rivarola-Duarte, L., Axenov-Gribanov, D.V., Bedulina, D.S., Gurkov, A.N., Drozdova, P., Timofeyev, M.A., Stadler, P.F., Luckenbach, T., Pörtner, H.-O., Sartoris, F.J., Lucassen, M. (2021):
Thermal reaction norms of key metabolic enzymes reflect divergent physiological and behavioral adaptations of closely related amphipod species
Sci. Rep. 11 , art. 4562
Volltext (DOI)
24089 Kasmanas, J.C., Bartholomäus, A., Borim Corrêa, F., Tal, T., Jehmlich, N., Herberth, G., von Bergen, M., Stadler, P.F., de Carvalho, A.C.P.L.F., Nunes da Rocha, U. (2021):
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes
Nucleic Acids Res. 49 (D1), D743 - D750
Volltext (DOI)
16938 Kolora, S.R.R., Faria, R., Weigert, A., Schaffer, S., Grimm, A., Henle, K., Sahyoun, A.H., Stadler, P.F., Nowick, K., Bleidorn, C., Schlegel, M. (2017):
The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. viridis
Mitochondrial DNA 28 (1), 116 - 118
Volltext (DOI)
25120 Kolora, S.R.R., Gysi, D.M., Schaffer, S., Grimm-Seyfarth, A., Szabolcs, M., Faria, R., Henle, K., Stadler, P.F., Schlegel, M., Nowick, K. (2021):
Accelerated evolution of tissue-specific genes mediates divergence amidst gene flow in European green lizards
Genome Biol. Evol. 13 (8), evab109
Volltext (DOI)
21629 Kolora, S.R.R., Weigert, A., Saffari, A., Kehr, S., Costa, M.B.W., Spröer, C., Indrischek, H., Chintalapati, M., Lohse, K., Doose, G., Overmann, J., Bunk, B., Bleidorn, C., Grimm-Seyfarth, A., Henle, K., Nowick, K., Faria, R., Stadler, P.F., Schlegel, M. (2019):
Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation
GigaScience 8 (2), giy160
Volltext (DOI)
22815 Ludwig, J., Höner zu Siederdissen, C., Liu, Z., Stadler, P.F., Müller, S. (2019):
flowEMMi: an automated model-based clustering tool for microbial cytometric data
BMC Bioinformatics 20 , art. 643
Volltext (DOI)
13718 Müller, S.A., Findeiß, S., Pernitzsch, S.R., Wissenbach, D.K., Stadler, P.F., Hofacker, I.L., von Bergen, M., Kalkhof, S. (2013):
Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics
J. Proteomics 86 , 27 - 42
Volltext (DOI)
10804 Müller, S.A., Kohajda, T., Findeiß, S., Stadler, P.F., Washietl, S., Kellis, M., von Bergen, M., Kalkhof, S. (2010):
Optimization of parameters for coverage of low molecular weight proteins
Anal. Bioanal. Chem. 398 (7-8), 2867 - 2881
Volltext (DOI)
22921 Nitsche, A., Arnold, C., Ueberham, U., Reiche, K., Fallmann, J., Hackermüller, J., Horn, F., Stadler, P.F., Arendt, T. (2020):
Alzheimer-related genes show accelerated evolution
Mol. Psychiatr.
Volltext (DOI)
16144 Nitsche, A., Rose, D., Fasold, M., Reiche, K., Stadler, P.F. (2015):
Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved
RNA 21 (5), 801 - 812
Volltext (DOI)
12072 Otto, W., Stadler, P.F., Prohaska, S.J. (2011):
Phylogenetic footprinting and consistent sets of local aligments
In: Giancarlo, R., Manzini, G. (eds.)
Combinatorial Pattern Matching : 22nd Annual Symposium, CPM 2011, Palermo, Italy, June 27-29, 2011. Proceedings
Lect. Notes Comput. Sci. 6661
Springer, Berlin, Heidelberg, New York, p. 118 - 131
Volltext (DOI)
22828 Petruschke, H., Anders, J., Stadler, P.F., Jehmlich, N., von Bergen, M. (2020):
Enrichment and identification of small proteins in a simplified human gut microbiome
J. Proteomics 213 , art. 103604
Volltext (DOI)
19367 Richards, C.L., Alonso, C., Becker, C., Bossdorf, O., Bucher, E., Colomé-Tatché, M., Durka, W., Engelhardt, J., Gaspar, B., Gogol-Döring, A., Grosse, I., van Gurp, T.P., Heer, K., Kronholm, I., Lampei, C., Latzel, V., Mirouze, M., Opgenoorth, L., Paun, O., Prohaska, S.J., Rensing, S.A., Stadler, P.F., Trucchi, E., Ullrich, K., Verhoeven, K.J.F. (2017):
Ecological plant epigenetics: Evidence from model and non-model species, and the way forward
Ecol. Lett. 20 (12), 1576 - 1590
Volltext (DOI)
14621 Rivarola-Duarte, L., Otto, C., Jühling, F., Schreiber, S., Bedulina, D.S., Jakob, L., Gurkov, A., Axenov-Gribanov, D., Sahyoun, A.H., Lucassen, M., Hackermüller, J., Hoffmann, S., Sartoris, F., Pörtner, H.-O., Timofeyev, M., Luckenbach, T., Stadler, P.F. (2014):
A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus
J. Exp. Zool. Part B 322 (3), 177 - 189
Volltext (DOI)
11359 Rose, D., Hiller, M., Schutt, K., Hackermüller, J., Backofen, R., Stadler, P.F. (2011):
Computational discovery of human coding and non-coding transcripts with conserved splice sites
Bioinformatics 27 (14), 1894 - 1900
Volltext (DOI)
22367 Shatilina, Z., Drozdova, P., Bedulina, D., Rivarola-Duarte, L., Schreiber, S., Otto, C., Jühling, F., Aulhorn, S., Busch, W., Lubyaga, Y., Kondrateva, E., Pobezhimova, T., Jakob, L., Lucassen, M., Sartoris, F.J., Hackermüller, J., Pörtner, H.-O., Stadler, P.F., Luckenbach, T., Timofeyev, M. (2020):
Transcriptome-level effects of the model organic pollutant phenanthrene and its solvent acetone in three amphipod species
Comp. Biochem. Physiol. D-Genomics Proteomics 33 , art. 100630
Volltext (DOI)
12135 Tramontano, A., Donath, A., Bernhart, S.H., Reiche, K., Böhmdorfer, C., Stadler, P.F., Bachmair, A. (2011):
Deletion analysis of the 3' long terminal repeat sequence of plant retrotransposon Tto1 identifies 125 base pairs redundancy as sufficient for first strand transfer
Virology 412 (1), 75 - 82
Volltext (DOI)
11144 Washietl, S., Findeiss, S., Müller, S.A., Kalkhof, S., von Bergen, M., Hofacker, I.L., Stadler, P.F., Goldmann, N. (2011):
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data
RNA 17 (4), 578 - 594
Volltext (DOI)
13925 Will, S., Siebauer, M.F., Heyne, S., Engelhardt, J., Stadler, P.F., Reiche, K., Backofen, R. (2013):
LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search
Algorithms Mol. Biol. 8 , art. 14
Volltext (DOI)
22592 Yazbeck, A.M, Stadler, P.F., Tout, K., Fallmann, J. (2019):
Automatic curation of large comparative animal MicroRNA datasets
Bioinformatics 35 (22), 4553 - 4559
Volltext (DOI)
21392 Yazbeck, A.M., Tout, K.R., Stadler, P.F., Hertel, J. (2017):
Towards a consistent, quantitative evaluation of microRNA evolution
J. Integr. Bioinform. 14 (1)
Volltext (DOI)
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